Merge pull request #192 from Artur-man/main

update dev, fix bugs update python dependencies

.github/workflows/check.yml

@@ -148,12 +148,25 @@ jobs:
       # All Other dependencies
       - name: Install Suggested dependencies
         run: |
+          install.packages(c('reticulate'))
+          BiocManager::install(c('basilisk'))
           BiocManager::install(c('DelayedArray'))
           BiocManager::install(c('HDF5Array'))
           remotes::install_github('bnprks/BPCells/[email protected]')
           devtools::install_github('BIMSBbioinfo/ImageArray')
           devtools::install_github('BIMSBbioinfo/HDF5DataFrame')
           devtools::install_github('BIMSBbioinfo/ZarrDataFrame')
+          install.packages("Seurat")
+          BiocManager::install("glmGamPoi")
+          install.packages('hdf5r')
+          BiocManager::install('RBioFormats')
+          BiocManager::install('ComplexHeatmap')
+          devtools::install_github('dmcable/spacexr')
+          devtools::install_github('xuranw/MuSiC')
+          BiocManager::install('SingleCellExperiment')
+          BiocManager::install('SpatialExperiment')
+          install.packages('dplyr')
+          BiocManager::install('DESeq2')
         shell: Rscript {0}
 
       ## R CMD Check

.github/workflows/docker.yml

@@ -0,0 +1,44 @@
+name: Publish Docker image
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    if: github.repository == 'BIMSBbioinfo/VoltRon'
+
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+      id-token: write
+
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: amanukyan1385/rstudio-voltron
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./inst/extdata/Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

DESCRIPTION

@@ -1,20 +1,19 @@
 Package: VoltRon
 Type: Package
-Title: VoltRon for Spatial Data Integration and Analysis
+Title: VoltRon for Spatial Omics Data Integration and Analysis
 Version: 0.2.0
 Depends: R (>= 4.3.0)
 Author: Artür Manukyan, Ella Bahry, Raj Prateek Rai, Wei-Che Ko, Deborah Schmidt, Markus Landthaler, Altuna Akalin
 Maintainer: Artür Manukyan <[email protected]>
-Description: VoltRon is a novel spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells and even molecules.
+Description: VoltRon is a novel spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells, molecules and event tiles.
 License: MIT + file LICENSE
 SystemRequirements: OpenCV 4.8 (or higher): libopencv-dev (Debian, Ubuntu) or opencv-devel (Fedora)
 Encoding: UTF-8
 RoxygenNote: 7.3.2
 biocViews:
-Imports: methods, S4Arrays, grDevices, data.table, EBImage, RcppAnnoy, RANN,
-         Matrix, dplyr, ggplot2, ggrepel, igraph, irlba, rjson, magick, ids, 
-         sp, reshape2, rlang, ggpubr, shiny, shinyjs, stringr, uwot, RCDT, 
-         basilisk, reticulate
+Imports: methods, grDevices, data.table, Matrix, S4Arrays, ids, RcppAnnoy, 
+         RANN, igraph, dplyr, ggplot2, ggrepel, ggpubr, rjson, magick, 
+         EBImage, sp, rlang, shiny, shinyjs, stringr, irlba, uwot, RCDT
 LinkingTo: Rcpp, RcppArmadillo (>= 0.4)
 Collate: 
     'RcppExports.R'
@@ -41,6 +40,7 @@ Collate:
     'spatial.R'
     'visualization.R'
 Suggests:
+    testthat (>= 3.0.0),
     SpatialExperiment,
     SingleCellExperiment,
     Seurat,
@@ -51,12 +51,14 @@ Suggests:
     RBioFormats,
     XML,
     ComplexHeatmap,
+    basilisk,
+    reticulate,
     xlsx,
+    reshape2,
     tiledb,
     tiledbsc,
     arrow,
     vitessceR,
-    testthat (>= 3.0.0),
     geojsonR,
     circlize,
     rstudioapi,

NAMESPACE

@@ -46,6 +46,7 @@ S3method(addAssay,vrMetadata)
 S3method(addFeature,VoltRon)
 S3method(addFeature,vrAssayV2)
 S3method(as.VoltRon,Seurat)
+S3method(as.VoltRon,SpatialExperiment)
 S3method(as.Zarr,"magick-image")
 S3method(as.Zarr,VoltRon)
 S3method(combineChannels,VoltRon)
@@ -191,8 +192,8 @@ export(formAssay)
 export(formImage)
 export(formVoltRon)
 export(generateCosMxImage)
-export(generateGeoJSONFromSegments)
-export(generateSegmentsFromGeoJSON)
+export(generateGeoJSON)
+export(generateSegments)
 export(generateTileData)
 export(generateXeniumImage)
 export(getClusters)
@@ -292,16 +293,13 @@ importFrom(Matrix,t)
 importFrom(RANN,nn2)
 importFrom(RCDT,delaunay)
 importFrom(RcppAnnoy,AnnoyEuclidean)
-importFrom(basilisk,BasiliskEnvironment)
-importFrom(basilisk,basiliskRun)
-importFrom(basilisk,basiliskStart)
-importFrom(basilisk,basiliskStop)
 importFrom(data.table,alloc.col)
 importFrom(data.table,as.data.table)
 importFrom(data.table,chmatch)
 importFrom(data.table,data.table)
 importFrom(data.table,fread)
 importFrom(data.table,is.data.table)
+importFrom(data.table,melt)
 importFrom(data.table,set)
 importFrom(data.table,setkey)
 importFrom(dplyr,"%>%")
@@ -351,6 +349,7 @@ importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,add_edges)
 importFrom(igraph,as_adjacency_matrix)
+importFrom(igraph,as_data_frame)
 importFrom(igraph,cluster_leiden)
 importFrom(igraph,components)
 importFrom(igraph,disjoint_union)
@@ -390,9 +389,6 @@ importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
-importFrom(reshape2,acast)
-importFrom(reshape2,melt)
-importFrom(reticulate,import)
 importFrom(rjson,fromJSON)
 importFrom(rlang,"%||%")
 importFrom(rlang,'!!')

R/annotation.R

@@ -439,9 +439,7 @@ annotateSpatialData <- function(object, label = "annotation", assay = NULL, anno
   shiny::runApp(
     shiny::shinyApp(ui, server, options = list(host = shiny.options[["host"]], port = shiny.options[["port"]], launch.browser = shiny.options[["launch.browser"]]),
                     onStart = function() {
-                      cat("Doing application setup\n")
                       onStop(function() {
-                        cat("Doing application cleanup\n")
                       })
                     })
   )

R/auxiliary.R

@@ -194,19 +194,19 @@ rownames(.dccMetadata[["protocolData"]])[rownames(.dccMetadata[["protocolData"]]
 # Basilisk Environment ####
 ####
 
-#' The Python Basilisk environment
+#' get the Python Basilisk environment
 #'
 #' Defines a conda environment via Basilisk, which is used to convert R objects to Zarr stores.
 #'
-#' @importFrom basilisk BasiliskEnvironment
-#'
 #' @keywords internal
 #'
 #' @noRd
-py_env <- basilisk::BasiliskEnvironment(
-  envname="VoltRon_basilisk_env",
-  pkgname="VoltRon",
-  packages=c(
+getBasilisk <- function(){
+
+  if(!requireNamespace('basilisk'))
+    stop("Please install basilisk package!: BiocManager::install('basilisk')")
+
+  basilisk.packages=c(
     "numpy==1.*",
     "pandas==1.*",
     "anndata==0.7.*",
@@ -219,11 +219,20 @@ py_env <- basilisk::BasiliskEnvironment(
     "zarr==2.*",
     "numcodecs==0.*",
     "tifffile==2024.2.12"
-  ),
-  pip=c(
+  )
+  basilisk.pip=c(
     "ome-zarr==0.2.1"
   )
-)
+
+  py_env <- basilisk::BasiliskEnvironment(
+    envname="VoltRon_basilisk_env",
+    pkgname="VoltRon",
+    packages=basilisk.packages,
+    pip=basilisk.pip
+  )
+
+  py_env
+}
 
 ####
 # Other Auxiliary tools ####
@@ -321,7 +330,7 @@ make_css <- function (..., file = NULL)
     css_string
   }
   else {
-    cat(css_string, file = file)
+    message(css_string, file = file)
     invisible(NULL)
   }
 }